Job ID = 6368354 SRX = SRX495034 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:37 prefetch.2.10.7: 1) Downloading 'SRR1198566'... 2020-06-16T00:19:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:10 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:10 prefetch.2.10.7: 1) 'SRR1198566' was downloaded successfully Read 22634552 spots for SRR1198566/SRR1198566.sra Written 22634552 spots for SRR1198566/SRR1198566.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:52 22634552 reads; of these: 22634552 (100.00%) were unpaired; of these: 3508055 (15.50%) aligned 0 times 16088612 (71.08%) aligned exactly 1 time 3037885 (13.42%) aligned >1 times 84.50% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3758201 / 19126497 = 0.1965 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:34:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:07: 1000000 INFO @ Tue, 16 Jun 2020 09:34:12: 2000000 INFO @ Tue, 16 Jun 2020 09:34:17: 3000000 INFO @ Tue, 16 Jun 2020 09:34:22: 4000000 INFO @ Tue, 16 Jun 2020 09:34:27: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:34:33: 6000000 INFO @ Tue, 16 Jun 2020 09:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:34:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:38: 7000000 INFO @ Tue, 16 Jun 2020 09:34:40: 1000000 INFO @ Tue, 16 Jun 2020 09:34:44: 8000000 INFO @ Tue, 16 Jun 2020 09:34:47: 2000000 INFO @ Tue, 16 Jun 2020 09:34:50: 9000000 INFO @ Tue, 16 Jun 2020 09:34:53: 3000000 INFO @ Tue, 16 Jun 2020 09:34:56: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:35:00: 4000000 INFO @ Tue, 16 Jun 2020 09:35:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:35:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:02: 11000000 INFO @ Tue, 16 Jun 2020 09:35:07: 5000000 INFO @ Tue, 16 Jun 2020 09:35:08: 12000000 INFO @ Tue, 16 Jun 2020 09:35:09: 1000000 INFO @ Tue, 16 Jun 2020 09:35:14: 6000000 INFO @ Tue, 16 Jun 2020 09:35:15: 13000000 INFO @ Tue, 16 Jun 2020 09:35:16: 2000000 INFO @ Tue, 16 Jun 2020 09:35:21: 14000000 INFO @ Tue, 16 Jun 2020 09:35:21: 7000000 INFO @ Tue, 16 Jun 2020 09:35:23: 3000000 INFO @ Tue, 16 Jun 2020 09:35:27: 15000000 INFO @ Tue, 16 Jun 2020 09:35:28: 8000000 INFO @ Tue, 16 Jun 2020 09:35:29: 4000000 INFO @ Tue, 16 Jun 2020 09:35:29: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:35:29: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:35:29: #1 total tags in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:35:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:30: #1 tags after filtering in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:31: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:35:31: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:31: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:35:31: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 16 Jun 2020 09:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:31: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 16 Jun 2020 09:35:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:35:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:35: 9000000 INFO @ Tue, 16 Jun 2020 09:35:36: 5000000 INFO @ Tue, 16 Jun 2020 09:35:42: 10000000 INFO @ Tue, 16 Jun 2020 09:35:43: 6000000 INFO @ Tue, 16 Jun 2020 09:35:49: 11000000 INFO @ Tue, 16 Jun 2020 09:35:49: 7000000 INFO @ Tue, 16 Jun 2020 09:35:56: 8000000 INFO @ Tue, 16 Jun 2020 09:35:56: 12000000 INFO @ Tue, 16 Jun 2020 09:35:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:02: 9000000 INFO @ Tue, 16 Jun 2020 09:36:03: 13000000 INFO @ Tue, 16 Jun 2020 09:36:09: 10000000 INFO @ Tue, 16 Jun 2020 09:36:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:16: 11000000 INFO @ Tue, 16 Jun 2020 09:36:17: 15000000 INFO @ Tue, 16 Jun 2020 09:36:19: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:36:19: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:36:19: #1 total tags in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:36:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:36:19: #1 tags after filtering in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:20: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:36:20: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:20: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:36:20: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 16 Jun 2020 09:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:20: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:20: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 16 Jun 2020 09:36:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:36:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:22: 12000000 INFO @ Tue, 16 Jun 2020 09:36:28: 13000000 INFO @ Tue, 16 Jun 2020 09:36:35: 14000000 INFO @ Tue, 16 Jun 2020 09:36:41: 15000000 INFO @ Tue, 16 Jun 2020 09:36:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:36:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:36:44: #1 total tags in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:36:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:36:44: #1 tags after filtering in treatment: 15368296 INFO @ Tue, 16 Jun 2020 09:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:45: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:36:45: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:45: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:36:45: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 16 Jun 2020 09:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:45: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:45: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 16 Jun 2020 09:36:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:36:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495034/SRX495034.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 1 millis CompletedMACS2peakCalling